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Open Access Publications from the University of California

Department of Plant Sciences

UC Davis
Cover page of The effect of the AltSB gene on root growth in nutrient solution of isogenic sorghum hybrids

The effect of the AltSB gene on root growth in nutrient solution of isogenic sorghum hybrids


AlTSB, a major gene of the Multidrug and Toxic Compound Extrusion (Mate) family confers tolerance to aluminum toxicity in sorghum. This gene is a transporter gene that is responsible for the exudation of citric acid in the presence of toxic level of aluminum in the soil. The citrate complexes with the toxic aluminum forming a nontoxic compound. During the past several years, isogenic sorghum breeding lines, both cytoplasmic male-sterile lines (A and B-lines) and fertility restoring pollinator lines (R-lines) for this AlTSB gene have been developed at Embrapa Maize and Sorghum. These isogenic lines for AlTSB were used to develop sixteen isogenic sorghum hybrids with zero, one and two alleles for tolerance to aluminum toxicity. These sixteen hybrids are essentially genetically equal but with variation in the dose of the AlTSB allele. Seedlings of these isogenic hybrids were evaluated for root growth in nutrient solution with 0, 11, 20, 27 and 39μM aluminum for seven days at four intervals (0, 3, 5, and 7days). One dose of the gene had a very significant effect on maintaining root growth up to a concentration of 27 μM aluminum. A second dose of the gene continued to have a positive effect for some of the isogenic hybrids confirming the effect of partial dominance for this gene. The presence of the AlTSB gene in sorghum cultivars used in regions with acid soils or subsoils will contribute to the development of a better and deeper root system and promote greater and more sustainable productivity.

Cover page of Potassium influenced phenylalanine ammonia-lyase, peroxidases and polyphenol oxidases in Fusarium graminearum infected maize (Zea mays L.)

Potassium influenced phenylalanine ammonia-lyase, peroxidases and polyphenol oxidases in Fusarium graminearum infected maize (Zea mays L.)


Potassium (K) fertilizer is important for the reduction of many plant diseases, e.g., stalk rot of maize (Zea mays L.). However, the mechanism by which potassium promotes resistance to pathogens is not completely understood. Fusarium graminearum, which is the main pathogen causing stalk rot in maize, was selected to study the effect of potassium on phenylalanine ammonia-lyase (PAL; EC, peroxidase (POD; EC and polyphenol oxidase (PPO; EC, at both the physiological and molecular level. Gene expression was quantified by real-time reverse transcription PCR (Q-RT-PCR) technology. The incidence of maize stalk rot was significantly reduced by K application. After inoculation with F. graminearum, the potassium concentration increased in susceptible organs. Potassium induced the expression of and sustained elevated activities of PAL, POD, and PPO when maize was inoculated with the pathogen. The expression of the corresponding genes was also stimulated by potassium. This study demonstrated that potassium addition enhanced maize resistance to stalk rot by activating the expression and activity of defense-related enzymes involved in phenol metabolism.

Cover page of Biofortifying <em>Brassica</em> with calcium (Ca) and magnesium (Mg)

Biofortifying Brassica with calcium (Ca) and magnesium (Mg)


Billions of people worldwide consume insufficient calcium (Ca) or magnesium (Mg) for adequate health. Dietary Ca and Mg intakes can potentially be increased through crop biofortification. Recently, we reported sufficient natural genetic variation and heritability in a leafy crop plant (Brassica oleracea; C-genome, 1n=9; cabbage, cauliflower, kale etc.) to indicate that genetic biofortification is feasible in vegetable Brassica. We also reported loci affecting shoot Ca and Mg concentration (shoot-Ca and Mg). Here, we extend the previous study to explore the closely related species B. rapa (A-genome, 1n=10; Chinese cabbage, pak choi, a more tractable species genetically, and the amphidiploid species B. napus(AC-genome, 1n=19; canola/oilseed rape etc.). Wide variation in shoot/leaf-Ca and Mg occurs among all three species. Shoot/leaf-Ca and Mg is significantly and highly heritable. Quantitative trait loci (QTL) affecting shoot/leaf Ca and Mg concentration occur in potentially paralogous regions of B. oleracea and B. rapa. If confirmed, allelic variation at such loci could be used in biofortification breeding programs for vegetable Brassica. As genome sequencing and marker generation improves, it will be possible to resolve these (and other) putative loci to the gene level. Further studies on the regulation, interaction and function of these genes will enable us to understand Ca and Mg dynamics in plants.

Cover page of Is the Taste of Strawberry fruits (Fragaria x ananassa Duch.) affected by Ammonium and Nitrate Nutrition?

Is the Taste of Strawberry fruits (Fragaria x ananassa Duch.) affected by Ammonium and Nitrate Nutrition?


Strawberries are one of the most popular fruits. Since only tasteful fruits are attractive for the consumers the improvement of strawberry quality has been brought into focus over the last few years. The contributors to strawberry flavor are sugars, organic acids, and various volatile substances, making up the odor. Fructose, glucose, and sucrose represent 99% of the sugars. About 97% of the organic acids are citric acid and malic acid. In these studies we investigate the effect of the macronutrient nitrogen on the concentration of organic acids in strawberry plants and the fruits. Plant metabolism is differentially affected if nitrogen is taken up as NH4+ or NO3-. A high NH4+ uptake leads to a decreased pH in the cytoplasm and has to be stabilized by a proton excretion and by decarboxylation of organic acids by malic enzyme. In contrast, during NO3- reduction OH- is produced causing an increased cytosolic pH. This activates the enzyme PEP-caboxylase, which leads to an enhanced synthesis of oxaloacetate that is reduced to malate. Malate can be directly translocated into the vacuoles or incorporated into the cytoplasmic pool of the organic acids of the citric-acid cycle. The results of hydrophonic and soil experiments indicate that the N-form has an effect on the vegetative plant organs, but it does not affect the quality of strawberry fruits.

Cover page of Integrated plant nutrient management on diversified cropping system in aqua-terrestrial ecosystem for yield potentiality, quality and rural sustainability

Integrated plant nutrient management on diversified cropping system in aqua-terrestrial ecosystem for yield potentiality, quality and rural sustainability


Balanced and integrated plant nutrient management is imperative in agricultural production system including its quality - more applicable to those of developing country in the world. Like arable land in wetland ecosystem, nitrogen and other essential key plant elements and its management is also an integral part for so many beneficial aquatic crops (food, non-food etc.). With this significant importance of IPNM, number of case studies were undertaken through TOT, TDET based integrated aquaculture research projects (NWDPRA, ICAR, DoLR, Govt. of India) suited to wetland ecosystem at different agro-climatic zones (NAZ, OAZ including Coastal zone) of Indian sub-continent. In field study, emphasize were paid for utilizing divergence of waste wetlands followed with adoption of improvised agro-techniques (IPN & its management) on nutritious, valuable and popular aquatic food crops [deep-water rice - Oryza sativa, water chestnut - Trapa bispinosa, makhana - Euryale ferox, water lily - Nymphaea and Colocasia] in rural farming community at different agro-zones. Major and other essential plant nutrients combined with organic (neem oilcake) and inorganic sources (N : P2O5 : K2O @ 20-60 : 30-40 : 20-40 kg ha–1) includes spray materials were considered in these extensive study. Production of rice grains (3.76 t ha–1), fresh nut of water chestnut (9.93 t ha–1), makhana seeds (3.24 t ha–1), stalks of water-lily (6.52 t ha–1) and corm includes stalk yield of Colocasia (86.8 t ha–1) including its nutritional quality was remarkably influenced with IPNM, even exhibited >2.5 folds, economically viable to the rural farming community.

Nitrogen retranslocation during senescence in plants


Nitrogen remobilization is essential for nitrogen economy at the whole plant level. 15N tracing experiments showed that the Arabidopsis leaf to leaf N-remobilisation at vegetative stage was mainly determined by leaf senescence severity while N-remobilisation from rosette to seeds is depending on harvest index (Diaz et al. 2008). N-remobilisation efficiency to the seeds was higher in N limiting conditions (Lemaître et al. 2008). In order to investigate natural variation of nitrogen uptake and remobilisation in Arabidopsis, a core collection of accessions was grown at low (N-) and high (N+) nitrate supplies. Plants were labelled using 15N nitrate and traits measured (15N partition, nitrogen concentrations, remobilisation, biomass, yield, flowering). Globally, it was observed that the late-flowering plants had higher vegetative biomass, lower seed biomass and heavier seeds at both N+ and N- conditions. As a result, the late-flowering genotypes had lower harvest index (HI), higher nitrogen harvest index (NHI), higher 15N partitioning in seeds (15NHI), and lower fertility. All the accessions studied responded to low nitrogen nutrition by decreasing plant biomass, by lowering the amount of residual nitrogen lost in the dry remains (N%DR), and by increasing N-remobilisation (15NHI) and allocation of post-labelling assimilated nitrogen to the seeds. The most striking results were provided by the 15N tracing experiments, demonstrating that the amount of 15N, first assimilated into the rosette, and further remobilised to the seeds, is highly dependent on sink/source biomass ratio, i.e. on harvest index. Trait variations allowed us to group accessions in different feature-classes and to detect genotypes showing opposite or extreme behaviours. Results provided will facilitate the choice of recombinant inbred line parents for further QTL experiments. N-remobilisation was investigated for mutants of interest, using the same labelling protocol than for accessions. References : Diaz et al. (2008) Plant Physiology 147 : 1437-1449 Lemaître et al. (2008) Plant Cell Physiology 49(7): 1056-1065

Nitrogen (and phosphorus) nutrition of a woody plant and its root associates: a post-genomic perspective


Trees differ fundamentally from annual plant species in that they are adapted to survive on a long time-scale. The sequencing of the poplar genome and the use of appropriate functional tools offer an unprecedented opportunity to highlight key and specific mechanisms that characterize woody species. Most particularly, the isolation and characterization of complete sets of genes encoding transporters for inorganic / organic N and for P will bring fundamental knowledge that will be used to tackle changes in capacities for N and P uptake and assimilation under natural conditions. Additionally, under natural conditions the majority of trees are believed to have ectomycorrhizal (ECM) associations (intimate symbiotic association between fungi and roots), which can have a significant role in the worldwide nitrogen and/or phosphorus cycle. This mycorrhizal status relies 1) on efficient uptake processes by the fungal partner 2) on the bidirectional transfer of nutrients between the two symbionts, which was first demonstrated by Melin and Nilsson >50 years ago. The recent sequencing of the Laccaria bicolor genome, together with that of poplar, will probably reveals key genes that are essential for symbiotic functions, and hence for tree physiology.

Agronomic approaches in biofortification of food crops with micronutrients


Zinc (Zn) and iron (Fe) deficiencies are well-documented public health issue affecting nearly half of the world population. Developing countries are among the worst affected from Zn and Fe deficiencies which result in number of serious health complications, such as impairments in brain function and mental development, high susceptibility to deadly infectious disease and high risk for anemia. Recent reports indicate that, for example, Zn deficiency is responsible for death of nearly 450 000 children under 5-years old, annually. Very low concentrations and poor bioavailability of Zn and Fe in the commonly consumed foods seem to be the main reason for widespread occurrence of micronutrient deficiencies in human populations. Cereal-based foods are most commonly consumed foods and contribute up to 75 % of the daily calorie intake in the rural parts of the developing countries. Zinc and Fe deficiencies are also common micronutrient deficiencies in agricultural soils limiting both crop production and nutritional quality

Breeding new cereal genotypes with high genetic capacity for grain accumulation of micronutrients is widely accepted and most sustainable solution to the problem. There are impressive progresses in breeding new genotypes for high micronutrient density. However, the breeding approach is a long-term process and may be affected from very low chemical solubility of Zn and Fe in soils due to high pH and low organic matter. Agronomy-related approaches offer short-term and complementary solutions to the Zn and Fe deficiency in human health and crop production. Soil amendments contributing to solubility of Zn and Fe in soil solution, cereal-legume intercropping systems, and soil and foliar application of micronutrient-containing fertilizers are well-documented agronomic tools which contribute to root uptake, shoot and grain accumulation of Fe and Zn.

Fertilizer strategy is a simple and effective agronomic practice to contribute grain concentrations of micronutrients. Increasing number of evidence is available showing that soil and especially foliar application of Zn fertilizers results in impressive enhancements in grain Zn concentration. In contrast, soil and foliar application of Fe fertilizers is not effective in increasing grain Fe concentration. In wheat, foliar application of ZnSO4 at later growth stages seems to be more effective in enhancing grain Zn concentration than the application at earlier growth stages. Late foliar application of Zn is also effective in higher accumulation of Zn in the endosperm part of grains compared to earlier application. Enrichment of commonly soil-applied fertilizers like urea with Zn seems to be also very helpful strategy in improving grain Zn concentration. Recently published results indicate that soil and/or foliar application of nitrogen fertilizers improve both root uptake and grain accumulation of Fe and Zn.

The results available indicate high potential of agronomic approaches for improving grain Zn and Fe concentrations. Agronomic practices mentioned are simple and easily applicable in many target countries with high incidence of micronutrient deficiencies. Combination of agronomic practices with breeding approach will ensure the plants to maximize grain accumulation of micronutrients. This paper will also summarize the results of a recently initiated global zinc fertilizer project in 10 countries under HarvestPlus program (

Phosphate Sensing in Root Development


Inadequate availability of inorganic phosphate (Pi) in the rhizosphere is a common challenge to plants, which activate metabolic and developmental responses to maximize Pi acquisition. The sensory mechanisms that monitor environmental Pi status and regulate root growth via altered meristem activity are unknown. We show that PHOSPHATE DEFICIENCY RESPONSE 2 (PDR2) encodes the single P5-type ATPase of Arabidopsis thaliana. PDR2 functions in the endoplasmic reticulum (ER) and is required for proper expression of SCARECROW (SCR), a key regulator of root patterning, and for stem cell maintenance in Pi-deprived roots. We further show that the multicopper oxidase encoded by LOW PHOSPHATE ROOT1 (LPR1) is targeted to the ER and that LPR1 and PDR2 interact genetically. Since the expression domains of both genes overlap in the stem cell niche and distal root meristem, we propose that PDR2 and LPR1 function together in an ER-resident pathway that adjusts root meristem activity to external Pi. Our data indicate that the Pi-conditional root phenotype of pdr2 is not caused by increased Fe availability in low Pi; however, Fe homeostasis modifies the developmental response of root meristems to Pi availability.

Cover page of Responses of Some Dwarf Bean (Phaseolus vulgaris L.) Genotypes Grown in Turkey to Zinc and Boron Applications

Responses of Some Dwarf Bean (Phaseolus vulgaris L.) Genotypes Grown in Turkey to Zinc and Boron Applications


This study was conducted to determine the effects of boron (B) and zinc (Zn) applications on biomass, dry weight content and grain yield of 25 registered and local populations of dwarf bean genotypes tested. Plants were grown for 3 B and 3 Zn doses (0, 5, 10 mg kg-1 each). The trial was conducted in three replicates within a controlled glasshouse according to randomized plots factorial design. Results have shown that B and Zn applications considerably effect on the dwarf dry bean varieties in terms of biomass, dry weight and grain yield. From the genotypes used, Eskisehir-855, Karacasehir-90, Noyanbey, Terzibaba, Yakutiye, Fasulye sira, Yalova-17, Romano, Nazende, Seminis Gina, Yunus-90, Akman-98, Z¨ulbiye, Horoz fasulye and Kanada were found to be resistant to B deficiency while Sehirali-90, G¨oyn¨uk-98, Akdag, Sahin-90, ¨Onceler-98, Aras-98, Sarikiz, Magnum, May Gina and Efsane were the sensitive ones. The highest grain yield at 10 mg B kg-1 application was attained from the species Aras-98 and Kanada, hence they were classified as resistant to B toxicity. Zinc x genotype interaction was found significant from the stand point of biomass, dry weight and grain yield. Akman-98, Karacasehir-90, Noyanbey, Terzibaba, Sahin-90, Horoz fasulye, Nazende and Efsane were tolerant to Zn deficiency, while G¨oyn¨uk-98, Aras-98 and Fasulye sira were moderately tolerant. On the other hand, the varieties Eskisehir-855, Yunus-90, Sehirali-90, ¨Onceler-98, Z¨ulbiye, Yakutiye, Romano and Kanada were moderately sensitive to Zn deficiency, while the species of Akdag, Sarikiz, Magnum, Seminis Gina, May Gina and Yalova-17 were highly sensitive.